Raw honeys contain diverse microbial communities, which have the potential to produce antimicrobial secondary metabolites. These naturally occurring antimicrobials are highly valuable for industry application. Investigating honey microbiome and metabolome can provide important information on factors influencing the microbial communities and antimicrobials produced. In our study, amplicon metagenomics was used to analyze the composition of microorganisms in raw honey and investigate environmental and physicochemical variables that are associated with different microbial communities. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. Important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. To obtain novel antimicrobials from natural sources, bacteria from raw honey were isolated and their antifungal-producing potential was evaluated. Naturally occurring antifungal secondary metabolites from these bacteria were further purified and identified. Using mass spectrometry and whole-genome sequence data, the main antifungal compound produced by two Bacillus velezensis isolates was determined as iturin A, a lipopeptide exhibiting broad spectrum antifungal activity. Results from this study provide important insights into the microbial communities associated with different types of raw honey and their antifungal metabolites. This research could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease. Currently, there is a high demand for natural, broad-spectrum, and eco-friendly bio-fungicides in the food industry. Naturally occurring antifungal products from food-isolated bacteria are ideal candidates for agricultural and food applications.